SUMMARY/ABSTRACT Respiratory viral infections contribute significantly to the morbidity and progressive decline in lung function experienced by patients with chronic lung diseases, such as cystic fibrosis (CF). Respiratory viral infections account for at least 50% of pulmonary exacerbations of adult CF patients and are linked to worsening of pulmonary function, antibiotic use, prolonged hospitalizations and increased respiratory symptoms. Clinical studies have also linked viral infections with the development of chronic infections, yet the underlying mechanisms are unknown. In this proposal, we will test the novel hypothesis that viral exacerbations alter the microbial composition of the upper and/or lower respiratory tract in CF, affecting both overall community diversity and function and impairing pulmonary function. This study is innovative and exploratory in nature and intended to lay the foundation for future studies to both uncover the molecular mechanisms underlying viral- bacterial interactions in the respiratory tract during chronic lung disease and also inform larger clinical studies that assess the impact of viral exacerbations on disease progression in CF and other chronic lung diseases. In the R61 phase of the award, we will use samples previously collected longitudinally over the course of one year from the sinonasal cavity of CF patients during endoscopic surgery. In Aim 1, we will determine if viral infections of the upper respiratory tract (URT) alter the microbial communities of the URT. In Aim 2, we will investigate potential mechanisms by which viral infections shape the microbial composition of the URT, focusing on skewed innate immune responses and altered nutritional immunity, as well as take an unbiased approach using ribosome profiling to assess functional pathways activated during viral infection that might shift the microbial communities of the URT. The R33 phase will build upon preliminary data and techniques adapted during the R61 phase to assess how viral infections alter the microbiome composition and function throughout the respiratory tract and if these alterations predict pulmonary function. Longitudinal, paired sinonasal and sputum samples will be collected every three months for two years. In Aim 3, we will examine if viral infections shift the microbial communities of the URT or LRT, as well as assess changes in innate immunity or nutritional immunity (i.e. elemental metals analysis) or microbial pathways activated that predict pulmonary function decline during viral infection. This phase will culminate in Aim 4 with mechanistic in vitro studies modeling key microbial interactions or pathways revealed in Aim 3, using our unique polymicrobial infection models with primary sinonasal and bronchial epithelial cells from CF patients. By elucidating mechanisms by which viral infections impact microbial communities in the respiratory tract, our long-term goal is to identify new therapeutic targets for intervention, as well as identify potential biomarkers to inform clinical care and predict disease progression.